[gmx-users] Regarding 'insolidangle' and some tools

[Venkat Reddy]

Thank you Sir. gmx help explains it. I tried to compile the tools on
gromacs-4.5 but somehow the installation was terminating with errors. Then
I thought, you might have the modified gromacs copy. Anyway, I will try to
install the tools on gromacs-4.5 template. Thank you sir for your time and
concern.


On Thu, Jul 10, 2014 at 9:51 AM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> Hi,
>
>
> On Wed, Jul 9, 2014 at 7:13 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:
>
> > underprot = insolidangle center com of lipids span group "Protein" cutoff
> > 5;
> >
> > I know the purpose of the above statement but I didn't get the meaning of
> > some of the words, like "insolidangle" and "cutoff=5". If don't mind, can
> > you please explain this statement?
> >
>
> Please see 'gmx help selections keywords insolidangle' for a general
> explanation. If that is not clear, I can clarify that further.
>
> There are some useful tools for spherical systems like g_jumpdist, g_rdf
> > (modified)....etc that you explained in your presentation. Do you have
> any
> > modified gromacs copy with the inclusion of these tools. Because these
> > tools are very important for my system. Sorry for such a lengthy mail.
> >
>
> I have sent whatever I had for these tools to you personally in May 2013.
> Not much has happened since, except that 'gmx distance', 'gmx gangle' and
> 'gmx sasa' may be able to cover some parts of the needs. Due to various
> reasons (most important of which is that I have left academia in 2010), it
> has not been exactly fast to get any of those tools actually included in
> Gromacs.
>
> I never had "modified Gromacs copy", but only a set of tools and the
> selection engine that could be compiled against an existing Gromacs
> installation. The selection engine was included in Gromacs 4.5, and the
> code has changed a lot since, but the tools have not been updated and so do
> not work with newer Gromacs versions without modifications.
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036